Human Gut Microbiota from Autism Spectrum Disorder Promote Behavioral Symptoms in Mice

Cell, Год журнала: 2019, Номер 177(6), С. 1600 - 1618.e17

Опубликована: Май 1, 2019

Язык: Английский

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ipyrad: Interactive assembly and analysis of RADseq datasets

Bioinformatics, Год журнала: 2019, Номер 36(8), С. 2592 - 2594

Опубликована: Дек. 31, 2019

Abstract Summary ipyrad is a free and open source tool for assembling analyzing restriction site-associated DNA sequence datasets using de novo and/or reference-based approaches. It designed to be massively scalable hundreds of taxa thousands samples, can efficiently parallelized on high performance computing clusters. available both as command line interface Python package with an application programming interface, the latter which used interactively write complex, reproducible scripts implement suite downstream analysis tools. Availability implementation program written in Python. Source code from GitHub repository (https://github.com/dereneaton/ipyrad/), Linux MacOS installs are distributed through conda manager. Complete documentation, including numerous tutorials, Jupyter notebooks demonstrating example assemblies applications tools online: https://ipyrad.readthedocs.io/.

Язык: Английский

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Tectonic collision and uplift of Wallacea triggered the global songbird radiation

Nature Communications, Год журнала: 2016, Номер 7(1)

Опубликована: Авг. 30, 2016

Abstract Songbirds (oscine passerines) are the most species-rich and cosmopolitan bird group, comprising almost half of global avian diversity. originated in Australia, but evolutionary trajectory from a single species an isolated continent to worldwide proliferation is poorly understood. Here, we combine first comprehensive genome-scale DNA sequence data set for songbirds, fossil-based time calibrations, geologically informed biogeographic reconstructions provide well-supported hypothesis group. We show that songbird diversification began Oligocene, accelerated early Miocene, at approximately age previous estimates. This burst occurred coincident with extensive island formation Wallacea, which provided dispersal corridor out resulted independent waves expansion through Asia rest globe. Our results reconcile evolution Earth history link major radiation terrestrial biodiversity within Australian continent.

Язык: Английский

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Practical considerations for plant phylogenomics

Applications in Plant Sciences, Год журнала: 2018, Номер 6(3)

Опубликована: Март 1, 2018

The past decade has seen a major breakthrough in our ability to easily and inexpensively sequence genome‐scale data from diverse lineages. development of high‐throughput sequencing long‐read technologies ushered the era phylogenomics, where hundreds thousands nuclear genes whole organellar genomes are routinely used reconstruct evolutionary relationships. As result, understanding which options best suited for particular set questions can be difficult, especially those just starting field. Here, we review most recent advances plant phylogenomic methods make recommendations project‐dependent practices considerations. We focus on costs benefits different approaches regard information they provide researchers address. also highlight unique challenges opportunities systems, such as polyploidy, reticulate evolution, use herbarium materials, identifying optimal methodologies each. Finally, draw attention lingering field reusability sets, look at some up‐and‐coming that may help propel even further.

Язык: Английский

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Global urban environmental change drives adaptation in white clover

Science, Год журнала: 2022, Номер 375(6586), С. 1275 - 1281

Опубликована: Март 17, 2022

Urbanization transforms environments in ways that alter biological evolution. We examined whether urban environmental change drives parallel evolution by sampling 110,019 white clover plants from 6169 populations 160 cities globally. Plants were assayed for a Mendelian antiherbivore defense also affects tolerance to abiotic stressors. Urban-rural gradients associated with the of clines 47% throughout world. Variation strength was explained changes drought stress and vegetation cover varied among cities. Sequencing 2074 genomes 26 revealed urban-rural best adaptive evolution, but degree adaptation Our results demonstrate urbanization leads at global scale.

Язык: Английский

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Taxonomic signatures of cause-specific mortality risk in human gut microbiome

Nature Communications, Год журнала: 2021, Номер 12(1)

Опубликована: Май 11, 2021

Abstract The collection of fecal material and developments in sequencing technologies have enabled standardised non-invasive gut microbiome profiling. Microbiome composition from several large cohorts been cross-sectionally linked to various lifestyle factors diseases. In spite these advances, prospective associations between health remained uncharacterised due the lack sufficiently representative population with comprehensive follow-up data. Here, we analyse long-term association variation mortality a well-phenotyped cohort Finland ( n = 7211). We report robust taxonomic functional signatures related Enterobacteriaceae family that are associated risk during 15-year follow-up. Our results extend previous cross-sectional studies, help establish basis for examining human composition, incident outcomes, general status.

Язык: Английский

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Standardized multi-omics of Earth’s microbiomes reveals microbial and metabolite diversity

Nature Microbiology, Год журнала: 2022, Номер 7(12), С. 2128 - 2150

Опубликована: Ноя. 28, 2022

Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure function microbial communities multiple habitats on a planetary scale. Here we present multi-omics analysis diverse set 880 community samples collected for Earth Microbiome Project. We include amplicon (16S, 18S, ITS) shotgun metagenomic sequence data, untargeted metabolomics data (liquid chromatography-tandem mass spectrometry gas chromatography spectrometry). used standardized protocols analytical methods to characterize communities, focusing relationships co-occurrences microbially related metabolites taxa environments, thus allowing us explore diversity at extraordinary In addition reference database metabolomic provide framework incorporating additional studies, enabling expansion existing knowledge form an evolving resource. demonstrate utility this by testing hypothesis that every microbe metabolite is everywhere but environment selects. Our results show exhibits turnover nestedness both environment, whereas relative abundances vary co-occur with specific consortia habitat-specific manner. additionally power certain chemistry, particular terpenoids, distinguishing Earth's environments (for example, terrestrial plant surfaces soils, freshwater marine animal stool), as well microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) Pantoea dispersa detritus). This Resource provides insight within from Earth, informing chemical ecology, foundation microbiome hosts environment.

Язык: Английский

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Gut Microbiome Composition Is Predictive of Incident Type 2 Diabetes in a Population Cohort of 5,572 Finnish Adults

Diabetes Care, Год журнала: 2022, Номер 45(4), С. 811 - 818

Опубликована: Янв. 31, 2022

To examine the previously unknown long-term association between gut microbiome composition and incident type 2 diabetes in a representative population cohort.We collected fecal samples from 5,572 Finns (mean age 48.7 years; 54.1% women) 2002 who were followed up for until 31 December 2017. The sequenced using shotgun metagenomics. We examined associations multivariable-adjusted Cox regression models. first used eastern Finland subpopulation to obtain initial findings validated these western subpopulation.Altogether, 432 cases of occurred over median follow-up 15.8 years. detected four species two clusters consistently associated with validation These Clostridium citroniae (hazard ratio [HR] 1.21; 95% CI 1.04-1.42), C. bolteae (HR 1.20; 1.04-1.39), Tyzzerella nexilis 1.17; 1.01-1.36), Ruminococcus gnavus 1.01-1.36). positively clusters, cluster 1 1.18; 1.02-1.38) 5 1.02-1.36), mostly consisted same species.We observed robust species-level taxonomic features predictive follow-up. build on extend previous mainly cross-sectional evidence further support links dietary habits, metabolic diseases, that are modulated by microbiome. can potentially be improve disease prediction uncover novel therapeutic targets diabetes.

Язык: Английский

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Prolonged morphological expansion of spiny-rayed fishes following the end-Cretaceous

Nature Ecology & Evolution, Год журнала: 2022, Номер 6(8), С. 1211 - 1220

Опубликована: Июль 14, 2022

Язык: Английский

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A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables

Nature Microbiology, Год журнала: 2024, Номер 9(3), С. 595 - 613

Опубликована: Фев. 12, 2024

Abstract Microbial breakdown of organic matter is one the most important processes on Earth, yet controls decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during despite selection effects location, climate season. We generated metagenome-assembled genome library from cadaver-associated soils integrated it with metabolomics data to identify links between taxonomy function. This universal decomposers characterized by cross-feeding metabolize labile products. The key bacterial fungal rare across non-decomposition environments appear unique decaying flesh, including humans, swine, mice cattle, insects as likely vectors for dispersal. observed lockstep interactions further underlies robust forensic tool potential aid predictions time since death.

Язык: Английский

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